Need help configuring a 5i25 with Gecko G540

I just installed a Mesa 5i25 card, flashed it for the G540, and commenced configuring PNCConfig, I have got some way in that I can test drive the stepper motors OK, If I leave out any homing I can go to the axis program and also drive the steppers back and forth.

However I am stuck on configuring the limit/home switches, in stepconf I had them set on pin 10 minimum limit + home X, pin 11 for Y and 12 for Z, I am trying to emulate these settings without any luck on I/O 3. I think I have the search direction and velocities correct (maybe not) but when I run it I cannot turn power on because I get Joint 2 limit errors.

Also I have no idea how to get my router to be controlled via pin 14 at 0-5v and 50Hz as the G540 requires.

I'm not sure what info I should provide to assist so some hand holding and guidance would be appreciated

thanks for the quick reply, I have already tried that with and without inverting, swapping them around in different gpio inputs, and nothing seems to make a difference, hence my posts.
I can post whatever files may help, I am just not sure which would be helpful.

Of course, here they are.
also I have been fiddling with settings and in stepconf I had all limit switches inversed, if I do that on pncconf I get all joints on limit error, no error if I uncheck the inv box, however I also get no feedback detected from the G540 when a limit is activated, there are other confusing issues which will have to wait.

I needed to change Min X + Home etc for each axis to Home X Home Y etc then hand edit the HAL file to change the GPIO numbers as you indicated.
This is now working in that I can turn the system on, home the axis as per the pncconfig file I created for each axis (when I remembered to switch from mm/s to mm/min) then move and touch off and run a job.

So a big thank you for that.

I would now like to control my spindle by setting the output on pin 14 to switch between 0-5v and 50Hz base PWM freq. (does the 0-5v depend on the PC's bus? mine is 3.3v) and also spindle on

Does your firmware have a PWM module on pin 14?
(I see from your PnCConf screenshot that you asked for it, but I am not clear which pin the PWM appears on. That is fixed by the firmware, and can be read from the --readhmid data.